Metagenomic Analysis: The Human Gut
Background: For many years it has been known by the scientific community that there are numerous microorganisms that live not only on us (that is our skin), but also within us. The relationship we have with these microorganisms is a mutualistic one, which means that we both benefit from it. Although a lot of microorganisms live on our skin, the most populated area of our body by these tiny creatures is in the distal end of our intestines. The human intestine is home to 1013 to 1014 microorganisms whose additive genome contains around 100 times as many genes as our own genome1. One could say we are more microorganism than we are human! Getting back to the idea that these microorganisms are our friends, they help us with many physiological functions such as: maturation of the immune system, modulation of responses to epithelial cell injury, balancing of energy, and supporting biotransformations that we are ill-equipped to perform on our own1. The study that is highlighted within this post is one that uses metagenomic techniques to try and identify and learn more about the many microorganisms living within our distal gut. Overview: For this particular study, the scientists analyzed about 78 million base pairs of unique DNA sequence and 2,062 PCR (polymerase chain reaction)-amplified 16''S'' ribosomal DNA sequences that were gathered from the fecal DNA of two healthy adult subjects1. After the DNA was sequenced from the fecal samples and the genes identified, it was compared to both known human genes and microbial genes to identify what microorganisms were present within the two subjects’ guts. Experiment: Technique: First, all of the DNA that was collected from the fecal samples was shotgun sequenced to determine that the DNA sequences were. Then, the DNA sequences were compared to public databases that had the sequences of human DNA, bacterial DNA, and archaeal DNA. By carrying out this technique, the scientists were able to identify which microorganisms were living within the human gut of the two subjects. Lastly, further analyses were carried out to see what the function of these microorganisms is within the human gut, which was done by COG analysis and KEGG pathway reconstructions1. Sequencing: The shotgun sequencing method was used within this experiment in order to see what types of DNA sequences were found within the samples. Although this method is primarily used to identify a single species genomes, it also worked within this experiment because once all the genomes were identified, the relative number of each genome was used to determine how much of each type of microorganism was present within the subjects’ guts. After the sequencing was complete, a total of 50,164 open reading frames were predicted from the data set and 19,866 were successfully matched to a database1. Overall, 580 matches were made to members of Archaea and 13,130 matches were made to members of Bacteria. All of the other sequences were either not matched within the known databases of were too ambiguous to use. Overall, two of the more abundant microorganisms discovered were Bifidobacterium longum and Methanobrevibacter smithii1. Phylotypes Discovered: Using 132 bacterial-length 16''S'' rDNA sequences, it was found that there were 72 different bacterial phylotypes and only one archaeal phylotype. The archaeal phylotype was M.Smithii, and the 72 bacterial phylotypes were assigned to either Firmicutes ''(62) or ''Actinobacteria ''(10)1. Most of the ''Firmicutes were assigned to the class Clostridia. Now that some of the microorganisms were identified, the next step was to see what their function within the human gut was. COG Analysis and KEGG Pathway Reconstruction: The purpose of both COG and KEGG analyses are to identify what type of enzymes are being supplied by the microorganisms found within the guts of the two samples. As shown by the top graph to the right (COG), enzymes responsible for carbohydrate, amino acid, nucleotide, and coenzyme transport and metabolism were all very high within both the samples. The bottom graph to the right (KEGG) shows that the bacteria within the gut are essential for nucleotide, amino acid, and glycan metabolism, and the archaea are essential for carbohydrate, amino acid, and glycan metabolism. This experiment was able to highlight the fact that these microorganisms living within the human gut are helping with many metabolic processes that occur within the human body on a daily basis. Conclusion: Metagenomic analyses are essential to figuring out the genetic information of different species of organisms. In the case of this experiment, not only were some microorganisms of the human gut identified, but also the gene production and functional attributes of the gut microorganisms were discovered. By keeping track of the types of microorganisms present within our bodies, we will be able to better understand why certain diseases occur and create better treatments for them. The scientists behind this particular experiment state that experiments like these can “provide a broader view of human biology, including new biomarkers for defining our health; new ways for optimizing our personal nutrition; new ways for predicting the bio-availability of orally administered drugs; and new ways to forecast our individual and societal predispositions to disorders such as infections with pathogens, obesity, and misdirected or maladapted host immune responses of the gut”1. Resources 1.Metagenomic Analysis of the Human Distal Gut Microbiome by Steven R. Gill, Mihai Pop, Robert T. DeBoy, Paul B. Eckburg, Peter J. Turnbaugh, Buck S. Samuel, Jeffrey I. Gordon, David A. Relman, Claire M. Fraser-Liggett, and Karen E. Nelson PMCID: PMC3027896 2. Wikipedia.org 3.Your Health Is the Result of a Symbiotic Relationship with 100 Trillion Bacteria by Dr. Mercola